Phylogeography of the Temminck’s Stint (Calidris temminckii): historical vicariance but little present genetic structure in a regionally endangered Palearctic wader

Aim We study the population differentiation and phylogeography of the Temminck’s Stint (Calidris temminckii). Specifically, we seek signs of past and present population size changes and dispersal events and evaluate management and conservation unit status of the populations. We also study the possibility of introgression as the origin of two mitochondrial DNA (mtDNA) lineages found and estimate the divergence time of the lineages. Location Northern Eurasia. Methods We analysed 583 bp of mtDNA control region domains I and II and 11 microsatellite loci from 13 localities throughout the breeding range. In addition, we used mitochondrial cytochrome c oxidase subunit I (COI), a barcoding gene, to search for signs of introgression. Results More population differentiation was found from microsatellites than from mtDNA, although differentiation was weak in both markers. Signs of past population growth were observed, in addition to more recent decline in some areas. Both control region and COI sequences revealed two maternal lineages coexisting in Fennoscandia and in north‐west Siberia. No signs of introgression were detected. Lineage divergence time was estimated to have occurred during the glacial periods of Pleistocene. Main conclusions Slight differences in mtDNA and microsatellite differentiation and diversity may reflect different features – such as the mutation rate and effective population size – of the markers used, or female‐biased dispersal pattern and high male site‐fidelity of the species. The coexistence of the two mitochondrial lineages is most likely a consequence of post‐glacial mixing of two refugial Pleistocene populations. Based on genetic information alone, global conservation concerns are not imminent. However, fast decline of a marginal Bothnian Bay population and the smallness and remoteness of a Central Yakutian population warrant conservation actions.     

Geographic variation in relict populations: genetics and phenotype of bush-cricket Pholidoptera frivaldskyi (Orthoptera) in Carpathians

A decreasing population size is often causing species extinction, however, relict species persisting in small-sized populations counter this. We analysed spatial genetic variation and past changes in population size at the maternally-inherited mitochondrial DNA level to clarify the origin of all recently known isolated populations of Pholidoptera frivaldskyi occurring in the range of Carpathian Mountains. Along with that we analysed also morphological variation as some phenotypic traits can retain useful information on population genetic structure. We found a relatively low genetic diversity within isolated populations as 778 bp COI gene sequences revealed only 13 unique haplotypes (n = 173 individuals from 10 populations). The spatial analysis of molecular variance identified three geographically homogenous genetic clusters (one in Slovakia and two in Romania) with a high level of differentiation among them, suggesting restricted gene flow, whilst Bayesian skyline simulation reconstructed a negative demographic change through evolutionary time. Inferred genetic pattern clearly coincides with differences in males’ colour phenotype as the extent of pigmentation on the lateral pronotum varied significantly among genetic lineages. We suggest that geographical variation in the species populations has relict-like character and their isolated occurrence is not a result of recent introduction events. Identification of ‘evolutionary units’ may help in the conservation and management of this rare insect species.     

How do Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus) coexist in sympatry under high‐elevation conditions on the Qinghai–Tibetan Plateau?

The Qinghai–Tibetan Plateau (QTP) has the highest elevations of all biodiversity hotspots. Difficulties involved in fieldwork at high elevations cause challenges in researching mechanisms facilitating species coexistence. Herein, we investigated Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus), the only two endemic Galliformes on the QTP, to understand species coexistence patterns and determine how they live in sympatry for the first time. We assembled occurrence data, estimated habitat suitability differences and the underlying factors between two species at different scales using ecological niche models. Niche overlap tests were used to investigate whether niche differences between these species allow for their coexistence. We found that elevation was the most important factor determining habitat suitability for both species. At the meso‐scale, two species have similar ecological niches with their suitable habitats lying predominantly along ridge crests. However, ridge crests were more influential for habitat suitability by L. lerwa than for that of T. tibetanus because the latter species ranges further afield than ridge crests. Thus, differences in habitat suitability between these species lead to habitat partitioning, which allows stable coexistence. At the macro‐scale, temperature and precipitation were major factors influencing habitat suitability differences between these species. Tetraogallus tibetanus extended into the hinterland of the QTP and occurred at higher elevations, where colder and drier alpine conditions are commonplace. Conversely, L. lerwa occurred along the southeastern margin of the QTP with a lower snow line, an area prone to rainy and humid habitats. Niche overlap analysis showed that habitat suitability differences between these species are not driven by niche differentiation. We concluded that the coexistence of these two pheasants under high‐elevation conditions could be an adaption to different alpine conditions.     

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri,Ranidae)

Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.     

Population genetic structure and geographical differentiation of burbot (Lota lota) in China

The burbot (Lota lota Linnaeus, 1758) is the only freshwater species of the family Gadidae. There is a longstanding controversy about taxonomic status of the burbot from the Amur River basin. It is necessary to investigate population genetic structure and geographical differentiation among burbot populations from the Irtysh River basin and Amur River basin by mitochondrial DNA nucleotide sequence analysis. A 572 bp segment of cytochrome b and 425 bp segment of control region gene were sequenced from 4 populations. The results showed that there was lower genetic diversity of burbot in China and highly significant genetic difference between populations in the Amur River basin (P < 0.01). Demographic analysis indicated that the burbot from the Amur River basin experienced population expansion (Cytb: F _S = ? 0.912 (P = 0.287), D = ? 0.399 (P = 0.375); CR: F _S = ?4.771 (P = 0.015), D = ?1.523 (P = 0.03)). The data of 4 populations in China combining with the published data representing the Eurasian and North American burbot, revealed three distinct phylogenetic lineages (labelled EB, NA, Amur).     

Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam

Clonorchiasis is a parasitic disease of high public health importance in many countries in southeastern Asia and is caused by the Chinese liver fluke Clonorchis sinensis. However, the genetic structure and demographic history of its populations has not been sufficiently studied throughout the geographic range of the species and available data are based mainly on partial gene sequencing. In this study, we explored the genetic diversity of the complete 1560 bp cytochrome c oxidase subunit 1 (cox1) gene sequence for geographically isolated C. sinensis populations in Russia and Vietnam, to our knowledge for the first time. The results demonstrated low nucleotide and high haplotype differentiation within and between the two compared regions and a clear geographical vector for the distribution of genetic diversity patterns among the studied populations. These results suggest a deep local adaptation of the parasite to its environment including intermediate hosts and the existence of gene flow across the species’ range. Additionally, we have predicted an amino acid substitution in the functional site of the COX1 protein among the Vietnamese populations, which were reported to be difficult to treat with praziquantel. The haplotype networks consisted of several region-specific phylogenetic lineages, the formation of which could have occurred during the most extensive penultimate glaciations in the Pleistocene Epoch. The patterns of genetic diversity and demographics are consistent with population growth of the liver fluke in the late Pleistocene following the Last Glacial Maximum, indicating the lack of a population bottleneck during the recent past in the species’ history. The data obtained have important implications for understanding the phylogeography of C. sinensis, its host-parasite interactions, the ability of this parasite to evolve drug resistance, and the epidemiology of clonorchiasis under global climate change.     

Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes

At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.     

Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa

We carried out a population genetic analysis of five southern African gemsbok (Oryx gazella) populations based on 530 bp of the mitochondrial control region and ten microsatellites in 75 individuals. Both markers show the high variability often observed in African bovids. Three of the populations which can be traced back to very small founding or current sizes do not show any signs of reduced variability compared to the remaining populations. The mitochondrial haplotypes form three distinct lineages which most likely originated in the Pleistocene when climate fluctuations led to periodical reduction and spreading of gemsbok habitat and which, today, are found throughout the distribution range. Bayesian microsatellite analyses yielded two groups, suggesting a more recent geographical differentiation following the admixture of the mtDNA lineages. Combining our sequences with available published data of the remaining oryx species allowed for a direct molecular comparison of O. gazella and O. beisa which have sometimes been considered a single species. The average genetic divergence between haplotypes from the two taxa was very high (39.9%), supporting their classification into two different species.     

Diversification across the Palaearctic desert belt throughout the Pleistocene: phylogeographic history of the Houbara–Macqueen's bustard complex (Otididae: Chlamydotis) as revealed by mitochondrial DNA

Studies on the influence of Pleistocene climatic fluctuations and associated habitat changes on arid‐adapted bird species living in the Holarctic region are comparatively rare. In contrast to temperate species, the populations of arid‐adapted avian species might be characterized by low genetic differentiation because periods of population isolation were associated with the short interglacial periods, while population expansion events might have occurred during the longer glacial periods when steppe‐like vegetation might have been prevalent. In this study, we tested this hypothesis in a widespread arid‐adapted taxon of the Palaearctic desert belt, the Houbara–Macqueen's bustard complex. The later includes the Houbara bustard Chlamydotis undulata, comprising the North African subspecies Chlamydotis u. undulata and Chlamydotis u. fuertaventurae from the Canary Islands, and the Asian Macqueen's bustard Chlamydotis macqueenii. A long fragment (1042 bp) of the Cyt‐b gene was investigated in 39 representatives of the two species to assess phylogenetic and phylogeographic patterns, and demographic history and to compute divergence time estimates using a Bayesian relaxed molecular clock approach based on different coalescent priors. While the two species are genetically distinct, we found little intraspecific genetic differentiation. The divergence time of the two species falls within a period of extreme aridity at around 0.9 million years ago, which most likely resulted in an east–west vicariance along the Arabo‐Saharan deserts. Differentiation within Houbara and Macqueen's bustard occurred later during the Middle to Upper Pleistocene, and as we have predicted, periods of range expansion were associated to the last glacial period at least in the Macqueen's bustard.     

Mitochondrial evidence uncovers a refugium for the fat dormouse (Glis glis Linnaeus, 1766) in Hyrcanian forests of northern Iran

Fat dormouse is a squirrel-like rodent which is closely tied to deciduous forest ecosystem in southwestern Eurasia. As such it is a valuable indicator of forest survival in refugia during glacial-interglacial periods. Previous phylogeographic analyses uncovered divergent fat dormouse lineages in southern refugia in Italy and the Balkans, but retrieved a surprisingly low overall genetic diversity across the majority of the species’ range. We explored 812 bp long fragment of a cytochrome b (cyt b) gene in ten fat dormice from refugial Hyrcanian forests in northern Iran. We identified 10 new cyt b haplotypes, which generated a total dataset of 28 fat dormouse haplotypes. The phylogenetic reconstruction clustered the new haplotypes into the Iranian lineage which hold a sister position against all other fat dormouse haplotypes from Europe and Asia Minor. The divergence between these lineages suggests a fragmentation event of an ancestral population at 5.76 mya (95% HPD = 3.21–8.92). This early evolutionary divergence was possibly triggered in the Middle East by dramatically divergent environmental conditions at the Messinian Salinity Crisis. The divergence clearly exceeds the intraspecific divergence, and is well within the range between congeneric rodent species. We suggest a long-term persistence of the Iranian lineage in the Hyrcanian refugium which is consitent with a high number of endemics along the southern Caspian coastal areas.     

Quaternary range dynamics and polyploid evolution in an arid brushland plant species (Melampodium cinereum,Asteraceae)

Pleistocene climatic fluctuations played a principal role for range formation and population history of many biota, including regions not directly affected by glaciations, such as the arid habitats of the southwestern United States and adjacent Mexico. Specifically, drought-adapted species are expected to have persisted during cooler and wetter periods in one or more refugia, resulting in lineage differentiation, from where they reached their current distribution after range expansion in the course of Holocene aridification. Here, we test this hypothesis using Melampodium cinereum (Asteraceae), a morphologically and cytologically variable species of dry brushlands of Texas and adjacent Mexico. In line with the hypothesized presence of several refugia, AFLP data provide strong evidence for the presence of geographically distinct genetic lineages, which, however, only partly agree with current intraspecific taxonomy. Despite multiple origins, tetraploids form a genetically cohesive group. The exclusive occurrence of tetraploids in a range parapatric to that of the diploids likely results from former geographic isolation of cytotypes, lending further support for the presence of Pleistocene refugia. Whereas plastid sequence data show a clear signal for the expected Holocene range and population expansion, they show little geographic structure and high levels of intrapopulational diversity. This may be due to lineage sorting during periods of population separation and/or substantial gene flow among populations via seeds, which has not been sufficient to erode the overall pattern of genetic divergence resulting from geographic isolation.     

Speciation in the Deep Sea: Multi-Locus Analysis of Divergence and Gene Flow between Two Hybridizing Species of Hydrothermal Vent Mussels

Background

Reconstructing the history of divergence and gene flow between closely-related organisms has long been a difficult task of evolutionary genetics. Recently, new approaches based on the coalescence theory have been developed to test the existence of gene flow during the process of divergence. The deep sea is a motivating place to apply these new approaches. Differentiation by adaptation can be driven by the heterogeneity of the hydrothermal environment while populations should not have been strongly perturbed by climatic oscillations, the main cause of geographic isolation at the surface.

Methodology/Principal Finding

Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis. The analysis revealed that (i) the two species have started to diverge approximately 0.760 million years ago, (ii) the B. azoricus population size was 2 to 5 time greater than the B. puteoserpentis and the ancestral population and (iii) gene flow between the two species occurred over the complete species range and was mainly asymmetric, at least for the chromosomal regions studied.

Conclusions/Significance

A long history of gene flow has been detected between the two Bathymodiolus species. However, it proved very difficult to conclusively distinguish secondary introgression from ongoing parapatric differentiation. As powerful as coalescence approaches could be, we are left by the fact that natural populations often deviates from standard assumptions of the underlying model. A more direct observation of the history of recombination at one of the seven loci studied suggests an initial period of allopatric differentiation during which recombination was blocked between lineages. Even in the deep sea, geographic isolation may well be a crucial promoter of speciation.     

Multilocus phylogeography of the Wedge-billed Woodcreeper Glyphorynchus spirurus (Aves,Furnariidae) in lowland Amazonia: Widespread cryptic diversity and paraphyly reveal a complex diversification pattern

Amazonian rivers function as important barriers to dispersal of Amazonian birds. Studying population genetics of lineages separated by rivers may help us to uncover the dynamics of biological diversification in the Amazon. We reconstructed the phylogeography of the Wedge-billed Woodcreeper, Glyphorynchus spirurus (Furnariidae) in the Amazon basin. Sampling included 134 individuals from 63 sites distributed in eight Amazonian areas of endemism separated by major Amazonian rivers. Nucleotide sequences were generated for five genes: two mtDNA genes (1047 bp for cyt b and 1002 bp for ND2) and three nuclear genes (647 bp from the sex-linked gene ACO, 319 bp from the intron of G3PDH, and 619 bp from intron 2 of MYO). In addition, 37 individuals were randomly selected from the Rondônia and Inambari areas of endemism for genomic fingerprinting, using five ISSR primers. Our results reveal allopatric and well-supported lineages within G. spirurus with high levels of genetic differentiation (p-distances 0.9–6.3%) across opposite banks of major Amazonian rivers. The multilocus phylogenetic reconstructions obtained reveal several incongruences with current subspecies taxonomy. Within currently recognized subspecies, we found high levels of both paraphyly and genetic differentiation, indicating deep divergences and strong isolation consistent with species-level differences. ISSR fingerprinting supports the existence of genetically differentiated populations on opposite sides of the Madeira River. Molecular dating suggests an initial vicariation event isolating populations from the Guiana center of endemism during the Late Miocene/Early Pliocene, while more recent events subdivided Brazilian Shield populations during the Lower Pleistocene.     

Shennongjia–Wushan Mountains—One cryptic glacial refugium introduced by the phylogeographical study of the Geometridae moth Ourapteryx szechuana Wehrli

The origin and evolution of biodiversity in the Shennongjia and Wushan Mountains, located in central China, are little known. In this study, we used Ourapteryx szechuana, which is widely distributed in China and northern Nepal, to explore whether these mountains acted as glacial refugia during climate oscillations of the Quaternary. In total, 192 samples of O. szechuana were collected throughout much of the distribution range. Phylogenetic analysis, molecular dating, demographic history reconstructions, and MAXENT were used to investigate the evolutionary history and differentiation mechanisms and predict the potential species distributions during four different periods. The phylogenetic tree and the star‐like median‐joining network strongly supported two reciprocally monophyletic and allopatric lineages. Lineage I was restricted to the Shennongjia and Wushan Mountains. The divergence time of O. szechuana from its sister species O. thibetaria was approximately 1.94 Ma. The differentiation processes of the two intraspecific lineages occurred at approximately 0.47 Ma. The demographic history reconstruction and the ecological niche model suggested that Lineage II experienced an expansion after the LGM (Last Glacial Maximum), whereas Lineage I did not experience any expansion. Our results suggested the Naynayxungla glaciation promoted the divergence of the two lineages by restricting them to different refugia. The valleys of the Shennongjia–Wushan Mountains may have kept stable and warm (thus ice‐free) environments during Quaternary glaciations, allowing this region to act as a glacial refugia. Our studies show that the Shennongjia and Wushan Mountains are likely to be important but little studied glacial refugia for the insect and thus worthy of more attention.

The Naynayxungla Glaciation promoted the divergence of the two lineages by restricting them to different refugia. The Shennongjia and Wushan Mountains are one important and easily neglected refugia for the insect groups and are worthy of more attention.     

Molecular Phylogeography and Evolutionary History of Poropuntius huangchuchieni (Cyprinidae) in Southwest China

Background

The evolution of the Yunnan Plateau’s drainages network during the Pleistocene was dominated by the intense uplifts of the Qinghai-Tibetan Plateau. In the present study, we investigated the association between the evolutionary histories of three main drainage systems and the geographic patterns of genetic differentiation of Poropuntius huangchuchieni.

Methodology/Principal Findings

We sequenced the complete sequences of mitochondrial control region for 304 specimens and the sequences of Cytochrome b gene for 15 specimens of the species P. huangchuchieni and 5 specimens of Poropuntius opisthoptera. Phylogenetic analysis identified five major lineages, of which lineages MK-A and MK-B constrained to the Mekong River System, lineages RL and LX to the Red River System, and lineage SW to the Salween River System. The genetic distance and network analysis detected significant divergences among these lineages. Mismatch distribution analysis implied that the population of P. huangchuchieni underwent demographic stability and the lineage MK-B, sublineages MK-A1 and LX-1 underwent a recent population expansion. The divergence of the 5 major lineages was dated back to 0.73–1.57 MYA.

Conclusions/Significance

Our results suggest that P. opisthoptera was a paraphyletic group of P. huangchuchieni. The phylogenetic pattern of P. huangchuchieni was mostly associated with the drainage’s structures and the geomorphological history of the Southwest Yunnan Plateau. Also the differentiation of the major lineages among the three drainages systems coincides with the Kunlun-Yellow River Movement (1.10–0.60 MYA). The genetic differentiation within river basins and recent demographical expansions that occurred in some lineages and sublineages are consistent with the palaeoclimatic oscillations during the Pleistocene. Additionally, our results also suggest that the populations of P. huangchuchieni had keep long term large effective population sizes and demographic stability in the recent evolutionary history, which may be responsible for the high genetic diversity and incomplete lineages sorting of Poropuntius huangchuchieni.     

Phylogeography of the Golden Jackal (Canis aureus) in India

The golden jackal (Canis aureus) is one of the most common and widely distributed carnivores in India but phylogeographic studies on the species have been limited across its range. Recent studies have observed absence of mitochondrial (mt) DNA diversity in European populations while some North African populations of golden jackal were found to carry gray wolf (Canis lupus lupaster) mtDNA lineages. In the present study, we sequenced 440 basepairs (bp) of control region (CR) and 412 bp of cytochrome b (cyt b) gene of mtDNA from 62 golden jackals sampled from India (n = 55), Israel (n = 2) and Bulgaria (n = 5), to obtain a total of eighteen haplotypes, comprising sixteen from India and one each from Israel and Bulgaria. Except for three previously described haplotypes represented by one cyt b and one CR haplotype both from India, and one CR haplotype from Bulgaria, all haplotypes identified in this study are new. Genetic diversity was high in golden jackals compared to that reported for other canids in India. Unlike the paraphyletic status of African conspecifics with the gray wolf, the Indian (and other Eurasian) golden jackal clustered in a distinct but shallow monophyletic clade, displaying no evidence of admixture with sympatric and related gray wolf and domestic dog clades in the region. Phylogeographic analyses indicated no clear pattern of genetic structuring of the golden jackal haplotypes and the median joining network revealed a star-shaped polytomy indicative of recent expansion of the species from India. Indian haplotypes were observed to be interior and thus ancestral compared to haplotypes from Europe and Israel, which were peripheral and hence more derived. Molecular tests for demographic expansion confirmed a recent event of expansion of golden jackals in the Indian subcontinent, which can be traced back ~ 37,000 years ago during the late Pleistocene. Our results suggest that golden jackals have had a potentially longer evolutionary history in India than in other parts of the world, although further sampling from Africa, the Middle East and south-east Asia is needed to test this hypothesis.     

Phylogeographic Analyses Strongly Suggest Cryptic Speciation in the Giant Spiny Frog (Dicroglossidae: Paa spinosa) and Interspecies Hybridization in Paa

Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east–west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.     

Significant genetic differentiation between the Yellow Sea and East China Sea populations of cocktail shrimp Trachypenaeus curvirostris revealed by the mitochondrial DNA COI gene

The cocktail shrimp Trachypenaeus curvirostris is an ecologically and economically important shrimp species in the Yellow Sea and East China Sea. However, there is no information about its population genetic structure. The population genetic structure and level of gene flow of T. curvirostris from the Yellow Sea and the East China Sea were studied with a 658-bp segment of mtDNA COI gene. In total, 85 individuals were collected from five locations and 13 haplotypes were obtained. The genetic variation of COI gene in five populations was moderate, giving an overall haplotype diversity of 0.6888 ± 0.0432 and nucleotide diversity of 0.0069 ± 0.0038. Conflicting to our expectation, significant genetic differentiation was detected in this species. The result revealed two genetically divergent lineages, displaying clear different geographical distributions in the studied area. The significant genetic differentiation between the Yellow Sea and East China Sea populations might be caused by the Yangtze River outflow. Mismatch distribution revealed that T. curvirostris had undergone population range expansion, possibly before 103,400–109,700 years ago in the last interglaciation, rejecting the sudden demographic expansion.     

Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae

Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.